The present invention relates generally to the molecular characterization of indigenous methane-producing microorganisms and defined assemblages thereof from hydrocarbon-bearing formations, such coal seams; and more specifically, to the analyses of environmental genomic data from such microorganisms, and the use of such data and microorganisms to enhance conversion and recovery of methane using stimulants identified by determining the presence of enzymes in pathways involved in the conversion of a hydrocarbon to methane.
Coalbed methane (CBM) is a source of natural gas produced either biologically or thermogenically in coal deposits. Biogenic production of CBM is the result of microbial metabolism and the degradation of coal with a subsequent electron flow among multiple microbial populations. Thermogenic production of CBM is the result of thermal cracking of sedimentary organic matter or oil, occurring later in coalification when temperatures rise above levels at which the methane-producing microorganisms can live. In coalbeds, pressure from overlying rock and surrounding water cause the CBM to bond to the surface of the coal and be absorbed into the solid matrix of the coal as free gas within micropores and cleats (natural fractures in the coal), as dissolved gas in water, as adsorbed gas held by molecular attraction on surfaces of macerals (organic constituents that comprise the coal mass), micropores, and cleats in the coal, and as absorbed gas within the molecular structure of the coal.
Coal is a sedimentary rock with various degrees of permeability, with methane residing primarily in the cleats. These fractures in the coal act as the major channels to allow CBM to flow. To extract the CBM, a steel-encased hole is drilled into the coal seam, which allows the pressure to decline due to the hole to the surface or the pumping of small amounts of water from the coalbed (dewatering). CBM has very low solubility in water and readily separates as pressure decreases, allowing it to be piped out of the well separately from the water. The CBM is then sent to a compressor station and into natural gas pipelines.
CBM represents a significant portion of the natural gas produced in the United States, estimated as providing approximately 10% of the natural gas supplies, or about 1.8 trillion cubic feet (TCF). International reserves provide enormous opportunity for future CBM production. Among the most productive areas is the San Juan Basin, located in Colorado and New Mexico. Based on such enormous reservoirs of CBM, minimal improvements in CBM recovery could thus result in significantly increased production from a well, and accordingly, a variety of methods are being developed to improve the recovery of CBM from coal seams.
Purely physical interventions can include optimizing drilling and fracturing methods. Other improvement methods involve the application of external factors directly onto the coalbeds. These include, for example, the injection of gases such as nitrogen (see, e.g., Shimizu, S., Akiyama, M., Naganuma, T., Fujioka, M., Nako, M. and Ishijima, Y. 2007. Molecular characterization of microbial communities in deep coal seam groundwater of northern Japan. Geobiology 5(4):423-433; U.S. Pat. No. 4,883,122) and CO2 (see, e.g., U.S. Pat. No. 5,402,847); and the injection of hot fluids such as water or steam (see, e.g., U.S. Pat. No. 5,072,990). Various methods are intended to increase the permeability of the coalbed seams either physically (see, e.g., U.S. Pat. No. 5,014,788) or chemically (see, e.g., U.S. Pat. No. 5,865,248).
More recently, improvement methods are being developed to enhance biogenic methane production from existing wells. U.S. Pat. No. 5,424,195 discloses the use of a consortium of microorganisms cultured in situ or on a coal-containing substrate to biologically convert coal to methane. PCT/GB2006/004443 (WO2007/060473) discloses methods of producing and using a culture of subterranean microorganisms. PCT/US2006/039352 (WO2008/041990) discloses methods and systems for stimulating biogenic production by introducing an injection fluid which facilitates anaerobic biological degradation of the non-liquid hydrocarbon layer by indigenous microorganisms. PCT/US2007/080161 (WO2008/042888) discloses methods comprising in situ heating of a non-liquid hydrocarbon layer to allow biogenic production of methane. U.S. Pat. No. 7,426,960 discloses methods to stimulate biogenic production of a metabolite with enhanced hydrogen content comprising injecting water into an opening to disperse a consortium of microorganisms therein. U.S. Pat. No. 6,543,535 discloses processes for stimulating the activity of microbial consortia in a hydrocarbon-bearing, subterranean formation to convert hydrocarbons to methane by using information obtained from analyzing components of the formation and characterizing the microorganisms of the consortia. Although U.S. Pat. No. 6,543,535 contemplates comparing isolated microorganisms to known microorganisms to establish phylogenetic identity to such known organisms, it does not disclose the identification or use of specific genes encoding enzymes involved in the biotransformation of coal to methane from methanogenic bacteria within the consortia, or the use of enzyme analysis to identify novel stimulants. U.S. Patent Application Publication No. 2008/0289816 discloses processes for introducing microorganisms to carbonaceous material in an anaerobic environment and for increasing biogenic hydrocarbon production comprising the use of amended formation water. U.S. Patent Application Publication No. 2008/0299635 discloses methods for stimulating methane production from a carbonaceous material with a methanogenic consortium. U.S. Patent Application Publication No. 2009/0023612 discloses methods of increasing biogenic production of fuel gas from carbonaceous material comprising the use of an anaerobic consortium including a Pseudomonas species. U.S. Patent Application Publication No. 2009/0023611 discloses isolated microbial consortia for biogenically producing methane from complex hydrocarbons comprising a Thermotoga species. U.S. Patent Application Publication No. 2008/0286855 discloses a method of increasing production of materials with enhanced hydrogen content comprising introducing a consortium comprising an isolated culture of Thermacetogenium phaeum. U.S. Pat. No. 7,416,879 discloses methods of stimulating biological activity of Thermacetogenium phaeum in a geologic formation comprising adding an amendment to the formation. U.S. Patent Application Publication No. 2008/0182318 discloses isolated microbial consortia for biogenic methane production comprising a Desulfuromonas species. U.S. Patent Application Publication No. 2007/0295505 discloses methods of stimulating biogenic production of a metabolic product with enhanced hydrogen content in a geologic formation that includes a carbonaceous material comprising providing a phosphorous compound to microorganisms therein. U.S. Patent Application Publication No. 2007/0261843 discloses methods of stimulating biogenic production of a metabolic product with enhanced hydrogen content in a geologic formation that includes a carbonaceous material comprising providing hydrogen and phosphorous compound to microorganisms therein. PCT/US2006/031723 (WO2007/022122) discloses systems for enhanced biogenic methane production comprising amending CBM water and other microbe-containing media, diminishing sulfate reduction competition, and enhancing organic matter concentrations.
Biogenic production of methane is the product of multiple possible enzymatic pathways that successively break down complex macromolecular, polycyclic, lignin-derived organic matter. For example, ligninolytic enzymes may include peroxidases (manganese peroxidase, lignin peroxidases, etc.), phenol oxidases (laccases), hydrolases, esterases, and oxidases (see, e.g., Fakoussa, R. M. and Hofrichter, M. 1999. Biotechnology and Microbiology of Coal Degradation. Appl. Microbiol. Biotechnol. 52:25-40). Once initial fragmentation occurs, enzymes involved in demethylation and ring cleavage, oxidation of aromatic and aliphatic moieties, and subsequent fermentation and methanogenesis pathways become involved. It is believed that microorganisms present in hydrocarbon-bearing formations, including methanogens, are obligate anaerobes.
There remains a need in the art to effectively stimulate biogenic production in hydrocarbon-bearing formations such as coal and to enhance the CBM productivity of existing wells. The present invention provides methods not only for the identification and use of microorganisms present in the formation environment, but for the identification of tailored interventions (such as stimulants that can be introduced into the environment to enhance the biogenic production of methane) after establishing the presence of specific gene products involved in metabolic pathways leading to methane production.